"Resetting" TFS

I started a project on Codeplex with the Visual Studio TFS client and kept it in sync fine. Then I stopped using TFS for a while as I was working with the source files on another computer (by copying the files).

I've since made a lot of changes to the source and moved a lot of things around into different directories, and I want to commit my changes back to the codeplex TFS server.

...except I can't. I'm not sure what I should be doing; the Merge command doesn't seem to do what I think it does, and when I try to work with the files the client downloads the old versions of everything and overwrites my much more recent local copies (!!).

So is there any way to "start again" or something so that the TFS server has my canonical source or something else to achieve the same effect?